check_terms_matrix: Check the effect of variables in matrix design

In HCGB-IGTP/HCGB.IGTP.DAnalysis: Useful in-house functions for multiple analysis

Check the effect of variables in matrix design

Description

When running DESeq2 you usually add multiple terms to the matrix design. Test the effect of them

Usage

check_terms_matrix(
  sampleSheet.given,
  countsGiven,
  list.terms,
  red.formula.given,
  list_of_cols,
  compID.given,
  comp.folder.given,
  int_threads = 2,
  gene.annot.df = NULL,
  shrinkage.given = "apeglm"
)

Arguments

sampleSheet.given	Samplesheet containing metadata information
countsGiven	Dataframe/matrix of counts
list.terms	List of terms from samplesheet to include in design matrix
red.formula.given	Design formula to use as naive and in reduction
compID.given	Tag name to include for each comparison
comp.folder.given	Absolute path to store results
int_threads	Number of threads to use
shrinkage.given	LFC shrinkage estimator provided. Available: apeglm, ashr or normal

HCGB-IGTP/HCGB.IGTP.DAnalysis documentation built on April 13, 2025, 12:03 a.m.